Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors.

ABSTRACT:

Background

Assays of multiple tumor samples frequently reveal recurrent genomic aberrations, including point mutations and copy-number alterations, that affect individual genes. Analyses that extend beyond single genes are often restricted to examining pathways, interactions and functional modules that are already known.

Methods

We present a method that identifies functional modules without any information other than patterns of recurrent and mutually exclusive aberrations (RME patterns) that arise due to positive selection for key cancer phenotypes. Our algorithm efficiently constructs and searches networks of potential interactions and identifies significant modules (RME modules) by using the algorithmic significance test.

Results

We apply the method to the TCGA col

SUBMITTER: Miller CA 

PROVIDER: S-EPMC3102606 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature